I overlooked the first error (below) though. Between callbacks to replay_cb and eval_cb I get a missing cell problem. Probably fixable through attaching the mesh somewhere, I'll let you know.
/// Replay#0 at 0 of up0:0:1:Forward, ||up0:0:1:Forward|| = 8.28722
Unable to extract common cell; missing cell definition in form or expression.
Traceback (most recent call last):
File "_ctypes/callbacks.c", line 314, in 'calling callback function'
File "/home/martinal/opt/fenics/dorsal-hpc-unstable-27022013/lib/python2.7/site-packages/libadjoint/libadjoint.py", line 544, in cfunc
output_c[0] = self(adjointer, timestep, dependencies, values)
File "/home/martinal/opt/fenics/dorsal-hpc-unstable-27022013/lib/python2.7/site-packages/dolfin_adjoint/functional.py", line 84, in __call__
return dolfin.assemble(functional_value)
File "/home/martinal/opt/fenics/dorsal-hpc-unstable-27022013/lib/python2.7/site-packages/dolfin/fem/assembling.py", line 169, in assemble
common_cell=common_cell)
File "/home/martinal/opt/fenics/dorsal-hpc-unstable-27022013/lib/python2.7/site-packages/dolfin/fem/form.py", line 56, in __init__
common_cell)
File "/home/martinal/opt/fenics/dorsal-hpc-unstable-27022013/lib/python2.7/site-packages/dolfin/compilemodules/jit.py", line 66, in mpi_jit
return local_jit(*args, **kwargs)
File "/home/martinal/opt/fenics/dorsal-hpc-unstable-27022013/lib/python2.7/site-packages/dolfin/compilemodules/jit.py", line 154, in jit
return jit_compile(form, parameters=p, common_cell=common_cell)
File "/home/martinal/opt/fenics/dorsal-hpc-unstable-27022013/lib/python2.7/site-packages/ffc/jitcompiler.py", line 77, in jit
return jit_form(ufl_object, parameters, common_cell)
File "/home/martinal/opt/fenics/dorsal-hpc-unstable-27022013/lib/python2.7/site-packages/ffc/jitcompiler.py", line 155, in jit_form
element_mapping = _compute_element_mapping(form, common_cell)
File "/home/martinal/opt/fenics/dorsal-hpc-unstable-27022013/lib/python2.7/site-packages/ffc/jitcompiler.py", line 106, in _compute_element_mapping
common_cell = extract_common_cell(form, common_cell)
File "/home/martinal/opt/fenics/dorsal-hpc-unstable-27022013/lib/python2.7/site-packages/ufl/algorithms/preprocess.py", line 416, in extract_common_cell
error("Unable to extract common cell; "\
File "/home/martinal/opt/fenics/dorsal-hpc-unstable-27022013/lib/python2.7/site-packages/ufl/log.py", line 154, in error
raise self._exception_type(self._format_raw(*message))
ufl.log.UFLException: Unable to extract common cell; missing cell definition in form or expression.
/// J evaluated #0: 0
I overlooked the first error (below) though. Between callbacks to replay_cb and eval_cb I get a missing cell problem. Probably fixable through attaching the mesh somewhere, I'll let you know.
/// Replay#0 at 0 of up0:0:1:Forward, ||up0:0:1:Forward|| = 8.28722 callbacks. c", line 314, in 'calling callback function' martinal/ opt/fenics/ dorsal- hpc-unstable- 27022013/ lib/python2. 7/site- packages/ libadjoint/ libadjoint. py", line 544, in cfunc martinal/ opt/fenics/ dorsal- hpc-unstable- 27022013/ lib/python2. 7/site- packages/ dolfin_ adjoint/ functional. py", line 84, in __call__ assemble( functional_ value) martinal/ opt/fenics/ dorsal- hpc-unstable- 27022013/ lib/python2. 7/site- packages/ dolfin/ fem/assembling. py", line 169, in assemble cell=common_ cell) martinal/ opt/fenics/ dorsal- hpc-unstable- 27022013/ lib/python2. 7/site- packages/ dolfin/ fem/form. py", line 56, in __init__ martinal/ opt/fenics/ dorsal- hpc-unstable- 27022013/ lib/python2. 7/site- packages/ dolfin/ compilemodules/ jit.py" , line 66, in mpi_jit martinal/ opt/fenics/ dorsal- hpc-unstable- 27022013/ lib/python2. 7/site- packages/ dolfin/ compilemodules/ jit.py" , line 154, in jit cell=common_ cell) martinal/ opt/fenics/ dorsal- hpc-unstable- 27022013/ lib/python2. 7/site- packages/ ffc/jitcompiler .py", line 77, in jit ufl_object, parameters, common_cell) martinal/ opt/fenics/ dorsal- hpc-unstable- 27022013/ lib/python2. 7/site- packages/ ffc/jitcompiler .py", line 155, in jit_form element_ mapping( form, common_cell) martinal/ opt/fenics/ dorsal- hpc-unstable- 27022013/ lib/python2. 7/site- packages/ ffc/jitcompiler .py", line 106, in _compute_ element_ mapping common_ cell(form, common_cell) martinal/ opt/fenics/ dorsal- hpc-unstable- 27022013/ lib/python2. 7/site- packages/ ufl/algorithms/ preprocess. py", line 416, in extract_common_cell martinal/ opt/fenics/ dorsal- hpc-unstable- 27022013/ lib/python2. 7/site- packages/ ufl/log. py", line 154, in error _type(self. _format_ raw(*message) ) UFLException: Unable to extract common cell; missing cell definition in form or expression.
Unable to extract common cell; missing cell definition in form or expression.
Traceback (most recent call last):
File "_ctypes/
File "/home/
output_c[0] = self(adjointer, timestep, dependencies, values)
File "/home/
return dolfin.
File "/home/
common_
File "/home/
common_cell)
File "/home/
return local_jit(*args, **kwargs)
File "/home/
return jit_compile(form, parameters=p, common_
File "/home/
return jit_form(
File "/home/
element_mapping = _compute_
File "/home/
common_cell = extract_
File "/home/
error("Unable to extract common cell; "\
File "/home/
raise self._exception
ufl.log.
/// J evaluated #0: 0